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tt_assm_assm_blastn_wnode.cwl
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tt_assm_assm_blastn_wnode.cwl
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#!/usr/bin/env cwl-runner
cwlVersion: v1.2
label: "assm_assm_blastn_wnode"
class: Workflow # task type
inputs:
asn_cache: Directory
gencoll_asn: File
ref_gencoll_asn: File
queries_gc_id_list: File
subjects_gc_id_list: File
# assm_assm_blastn_wnode inputs:
compart: boolean?
evalue: float?
gapextend: int?
gapopen: int?
gc_cache: File
gc_seq_cache: Directory
max_bases_per_call: int?
max_target_seqs: int?
merge_align_filter: string?
merge_engine: string?
soft_masking: string?
task: string
use_common_components: boolean
window_size: int?
word_size: int?
workers_per_cpu: float?
nogenbank: boolean?
# gpx_qsubmit settings
affinity: string
outputs:
blast_align:
type: File
outputSource: gpx_qdump/output
steps:
assm_assm_blastn_create_jobs:
run: ../progs/assm_assm_blastn_create_jobs.cwl
in:
affinity_bin:
default: 10
queries_gc_id_list: queries_gc_id_list
subjects_gc_id_list: subjects_gc_id_list
out: [output]
gpx_qsubmit:
run: ../progs/gpx_qsubmit-xml.cwl
in:
affinity: affinity
asn_cache:
source: [asn_cache]
linkMerge: merge_flattened
nogenbank: nogenbank
xml_jobs: assm_assm_blastn_create_jobs/output
out: [jobs]
assm_assm_blastn_wnode:
run: ../progs/assm_assm_blastn_wnode.cwl
in:
target_set:
source: [gencoll_asn, ref_gencoll_asn]
linkMerge: merge_flattened
asn_cache:
source: [asn_cache, gc_seq_cache]
linkMerge: merge_flattened
compart: compart
evalue: evalue
gapextend: gapextend
gapopen: gapopen
gc_cache: gc_cache
max_bases_per_call: max_bases_per_call
max_target_seqs: max_target_seqs
merge_align_filter: merge_align_filter
merge_engine: merge_engine
soft_masking: soft_masking
task: task
use_common_components: use_common_components
window_size: window_size
word_size: word_size
workers_per_cpu: workers_per_cpu
input_jobs: gpx_qsubmit/jobs
out: [ outdir ]
gpx_qdump:
run: ../progs/gpx_qdump.cwl
in:
input_path: assm_assm_blastn_wnode/outdir
unzip:
default: '*'
out: [ output ]